@teselagen/ove 0.7.27 → 0.7.28

package/annotationsToSupport.js

@@ -0,0 +1,104 @@
+import createAction from "./utils/createMetaAction";
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+
+//this determines whether or not to
+const initialSupportedTypes = {
+  parts: true,
+  features: true,
+  translations: true,
+  primers: true,
+  cutsites: true,
+  orfs: true,
+  warnings: true,
+  assemblyPieces: true,
+  lineageAnnotations: true
+};
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const annotationSupportToggle = createAction("annotationSupportToggle");
+//eg: annotationSupportToggle('features')
+export const annotationSupportOn = createAction("annotationSupportOn");
+export const annotationSupportOff = createAction("annotationSupportOff");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createMergedDefaultStateReducer(
+  {
+    [annotationSupportToggle]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: !state[payload]
+      };
+    },
+    [annotationSupportOn]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: false
+      };
+    },
+    [annotationSupportOff]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: true
+      };
+    }
+  },
+  initialSupportedTypes
+);
+
+// import createAction from "./utils/createMetaAction";
+// import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+
+// //this determines whether or not to
+// const initialSupportedTypes = {
+//   parts: true,
+//   features: true,
+//   translations: true,
+//   primers: true,
+//   cutsites: true,
+//   orfs: true,
+//   warnings: true,
+//   assemblyPieces: true,
+//   lineageAnnotations: true
+// };
+
+// // ------------------------------------
+// // Actions
+// // ------------------------------------
+// export const annotationSupportToggle = createAction(
+//   "ANNOTATION_SUPPORT_TOGGLE"
+// );
+
+// export const annotationSupportOn = createAction("ANNOTATION_SUPPORT_ON");
+// export const annotationSupportOff = createAction("ANNOTATION_SUPPORT_OFF");
+
+// export default function (state = initialSupportedTypes, action) {
+//   switch (action.type) {
+//     case "ANNOTATION_SUPPORT_TOGGLE":
+//       return {
+//         ...state,
+//         [action.payload]: !state[action.payload]
+//       };
+//     case "ANNOTATION_SUPPORT_ON":
+//       return {
+//         ...state,
+//         [action.payload]: true
+//       };
+//     case "ANNOTATION_SUPPORT_OFF":
+//       return {
+//         ...state,
+//         [action.payload]: false
+//       };
+//     default:
+//       if (action.mergeStateDeep) {
+//         return {
+//           ...initialSupportedTypes,
+//           ...state
+//         };
+//       }
+//       return state;
+//   }
+// }

package/arrayToObjWithIds.js

@@ -0,0 +1,17 @@
+//helper function to make sure any arrays coming in
+
+import shortid from "shortid";
+
+//get converted to objects with unique ids
+export default function arrayToObjWithIds(array) {
+  const newObj = {};
+  array.forEach(function (item) {
+    const newItem = {
+      ...item,
+      id: item.id || shortid()
+    };
+    newObj[newItem.id] = newItem;
+  });
+
+  return newObj;
+}

package/arrayUtils.js

@@ -0,0 +1,19 @@
+export function insertItem(array, item, index) {
+  return [...array.slice(0, index), item, ...array.slice(index)];
+}
+
+export function removeItem(array, i) {
+  return array.filter((_, j) => j !== Number(i));
+}
+
+export function getLowerCaseObj(obj = {}) {
+  let key;
+  const keys = Object.keys(obj);
+  let n = keys.length;
+  const newobj = {};
+  while (n--) {
+    key = keys[n];
+    newobj[key.toLowerCase()] = obj[key];
+  }
+  return newobj;
+}

package/array_move.js

@@ -0,0 +1,10 @@
+export function array_move(arr, old_index, new_index) {
+  if (new_index >= arr.length) {
+    let k = new_index - arr.length + 1;
+    while (k--) {
+      arr.push(undefined);
+    }
+  }
+  arr.splice(new_index, 0, arr.splice(old_index, 1)[0]);
+  return arr; // for testing
+}

package/calculateTickMarkPositionsForGivenRange.js

@@ -0,0 +1,47 @@
+import { normalizePositionByRangeLength as norm } from "@teselagen/range-utils";
+import { getRangeLength } from "@teselagen/range-utils";
+
+export default function calculateTickMarkPositionsForGivenRange({
+  tickSpacing: _tickSpacing = 10,
+  range,
+  sequenceLength,
+  isProtein,
+  increaseOffset
+}) {
+  if (sequenceLength === 0) {
+    return [];
+  }
+  let tickSpacing = _tickSpacing;
+  if (isProtein) {
+    tickSpacing = Math.floor((_tickSpacing / 2) * 3);
+  }
+
+  const rangeLength = getRangeLength(range, sequenceLength);
+
+  let spacer = 0;
+  if (increaseOffset) {
+    spacer = range.start;
+  }
+  const firstTickOffsetFromRangeStart =
+    spacer + tickSpacing - (range.start % tickSpacing);
+
+  const tickMarks = [];
+  if (range.start === 0) tickMarks.push(isProtein ? 2 : 0);
+  let hasCrossedOrigin;
+  for (
+    let tick = firstTickOffsetFromRangeStart - 1;
+    tick < spacer + rangeLength;
+    tick += tickSpacing
+  ) {
+    let normed = norm(tick, sequenceLength);
+    if (!hasCrossedOrigin && normed < tick) {
+      if (!(normed % 10) && normed !== 0) {
+        tick = tick - 1;
+        normed = normed - 1;
+      }
+      if (normed !== 0) hasCrossedOrigin = true;
+    }
+    tickMarks.push(normed);
+  }
+  return tickMarks;
+}

package/caretPosition.js

@@ -0,0 +1,27 @@
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const caretPositionClear = createAction("CARET_POSITION_CLEAR");
+export const caretPositionUpdate = createAction("CARET_POSITION_UPDATE");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    SELECTION_LAYER_UPDATE: () => {
+      //clear the caret if the selection layer is updated!
+      return -1;
+    },
+    [caretPositionClear]: () => {
+      return -1;
+    },
+    [caretPositionUpdate]: (unused, payload) => {
+      return typeof payload === "string" ? parseInt(payload, 10) : payload;
+    }
+  },
+  -1
+);

package/cdsFeaturesSelector.js

@@ -0,0 +1,9 @@
+import { createSelector } from "reselect";
+import { filter } from "lodash-es";
+import featuresSelector from "./featuresSelector";
+
+function cdsFeaturesRawSelector(features) {
+  return filter(features, ({ type }) => type && type.toUpperCase() === "CDS");
+}
+
+export default createSelector(featuresSelector, cdsFeaturesRawSelector);

package/charWidth.js

@@ -0,0 +1,22 @@
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const updateSequenceSpacing = createAction("updateSequenceSpacing");
+
+const newVal = window.localStorage.getItem("charWidth");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [updateSequenceSpacing]: (state, payload) => {
+      localStorage.setItem("charWidth", payload);
+      return payload;
+    }
+  },
+  newVal || 9
+);

package/circular.js

@@ -0,0 +1,19 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const _updateCircular = createAction("UPDATE_CIRCULAR");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [_updateCircular]: (state, payload) => {
+      return payload;
+    }
+  },
+  true
+);

package/circularSelector.js

@@ -0,0 +1,4 @@
+import sequenceDataSelector from "./sequenceDataSelector";
+export default function (state) {
+  return sequenceDataSelector(state).circular;
+}